A Novel G-Quadruplex Binding Protein Determines the Boundaries of Genome Rearrangements in Tetrahymena thermophila

Date of Award

Summer 8-15-2013

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Microbiology & Microbial Pathogenesis)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Cells go to great lengths to control recombination in order to preserve genetic stability. During development of the somatic genome of the ciliate Tetrahymena thermophila, thousands of internal eliminated sequences (IESs) are excised from the germline-line derived DNA of the developing somatic nucleus. Precise elimination of these sequences is vital for keeping the genome intact during this process. We have identified a protein, Lia3, that acts in a novel way to control the boundaries of genome-wide DNA elimination events. The eliminated sequences are identified by small RNA directed heterochromatin formation; however, the boundaries of these IESs are determined by cis-acting flanking sequences. In cells lacking LIA3 (ΔLIA3), excision of the M IES is aberrant. Flanking polypurine tracts regulate the excision boundaries of the M IES. We found that excision of other IESs flanked by polypurine tracts is also imprecise in ΔLIA3 matings. Synthetic oligonucleotides containing these polypurine tracts form G-quadruplexes in vitro. and Lia3 preferentially binds this structure. Lia3 has three homologues in Tetrahymena that share a 100 amino acid conserved region. We propose that Lia3 and the three Lia3 related proteins all function to control the excision boundaries of specific subsets of IESs based on the cis-acting sequences flanking each IES. For Lia3, we hypothesize that this happens coincident with transcription that occurs across the polypurine tracts just prior to IES excision. The transcription opens up the DNA and allows a RNA/DNA hybrid quadruplex to form between the two ends of the IES. Lia3 binds this quadruplex and in doing so dictates the location of the excision boundaries, thereby linking G-quadruplex formation to IES excision.


English (en)

Chair and Committee

Douglas L Chalker

Committee Members

Sarah C. R Elgin, Joseph M Jez, Sheila A Stewart, Ting Wang Wang, Hani Zaher


Permanent URL: https://doi.org/10.7936/K7WM1BBH

This document is currently not available here.